Added source file location annotations to Metamorph DOM.

When debugging Metamorph scripts it is helpful to be able to link the
data, collector and function objects with their definition in the
Metamorph script. This commit annotates the XML DOM that is used to
build the actual metamorph object structure with location information
about location of each node in the source XML file.

The location information is attached as user data to element nodes using
the key `http://culturegraph.org/mf/user_data/location` (available via
`Location.USER_DATA_ID`). It contains start and end positions of the
element in the source file.

Implementing this functionality required a complete rewrite of the
`DOMLoader` because location information is only available from the SAX
parser and not from the DOM builder. Therefore the, implementation
uses a `Transformer` to construct a DOM from SAX events. The idea for
this implementation comes from
http://javacoalface.blogspot.de/2011/04/line-and-column-numbers-in-xml-dom.html

In the process of reimplementing the `DOMLoader` it was decided to move
the class and its helper classes out of the morph package and into its
own utility package due to the number of classes. Since we now have a
`util.xml` package the old `XMLUtil` class was moved into this package
as well.

Note: The default SAX implementation used by OpenJDK 1.7.0.60 includes
an old version of Xerces-J (2.7.1) which does not report location
information in x-included files correctly. A bug report for updating the
implementation exists (see https://bugs.openjdk.java.net/browse/JDK-8038043).
However, until this makes it into OpenJDK a newer version of Xerces needs
to be added manually to the classpath.

Author: cboehme

src/main/java/org/culturegraph/mf/morph/AbstractMetamorphDomWalker.java

@@ -28,6 +28,7 @@
 import org.culturegraph.mf.types.ScopedHashMap;
 import org.culturegraph.mf.util.ResourceUtil;
 import org.culturegraph.mf.util.StringUtil;
+import org.culturegraph.mf.util.xml.DomLoader;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NamedNodeMap;

src/main/java/org/culturegraph/mf/morph/DomLoader.java

@@ -26,8 +26,8 @@
 import org.culturegraph.mf.stream.sink.EventList;
 import org.culturegraph.mf.stream.sink.StreamValidator;
 import org.culturegraph.mf.util.ResourceUtil;
-import org.culturegraph.mf.util.XMLUtil;
 import org.culturegraph.mf.util.reflection.ObjectFactory;
+import org.culturegraph.mf.util.xml.XmlUtil;
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 
@@ -166,8 +166,8 @@ private java.io.Reader getDataFromSource(final String src) {
 	private java.io.Reader getDataEmbedded(final Element input) {
 		final String inputType = input.getAttribute(TYPE_ATTR);
 		if (input.hasChildNodes()) {
-			if (XMLUtil.isXmlMimeType(inputType)) {
-				return new StringReader(XMLUtil.nodeListToString(input.getChildNodes()));
+			if (XmlUtil.isXmlMimeType(inputType)) {
+				return new StringReader(XmlUtil.nodeListToString(input.getChildNodes()));
 			}
 			return new StringReader(input.getTextContent());
 		}

src/main/java/org/culturegraph/mf/test/TestCase.java

@@ -33,7 +33,7 @@
 
 /**
  * @author Christoph Böhme <[email protected]>, Markus Michael Geipel
- * 
+ *
  */
 public final class ResourceUtil {
 
@@ -44,7 +44,7 @@ private ResourceUtil() {
 	/**
 	 * first attempts to open resource with name 'name'. On fail attempts to
 	 * open file.
-	 * 
+	 *
 	 * @param name
 	 * @return
 	 * @throws FileNotFoundException
@@ -89,10 +89,14 @@ public static Reader getReader(final File file, final String encoding) throws Fi
 		return new InputStreamReader(getStream(file), encoding);
 	}
 
+	public static URL getResourceUrl(final String name) {
+		return Thread.currentThread().getContextClassLoader().getResource(name);
+	}
+
 	public static Properties loadProperties(final String location) {
 		try {
 			return loadProperties(getStream(location));
-		} catch (IOException e) {
+		} catch (final IOException e) {
 			throw new MetafactureException("'" + location + "' could not be loaded", e);
 		}
 	}
@@ -107,7 +111,7 @@ public static Properties loadProperties(final InputStream stream) throws IOExcep
 	public static Properties loadProperties(final URL url) {
 		try {
 			return loadProperties(url.openStream());
-		} catch (IOException e) {
+		} catch (final IOException e) {
 			throw new MetafactureException("'" + url.getPath() + "' could not be loaded", e);
 		}
 	}

src/main/java/org/culturegraph/mf/util/ResourceUtil.java

@@ -0,0 +1,50 @@
+/*
+ *  Copyright 2014 Christoph Böhme
+ *
+ *  Licensed under the Apache License, Version 2.0 the "License";
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+package org.culturegraph.mf.util.xml;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.XMLReader;
+
+/**
+ * Filters out CDATA events.
+ *
+ * Note that the actual contents of the CDATA section is
+ * not filtered. This filter removes only the events
+ * marking the start and end of CDATA sections. Their
+ * contents are still passed as {@code characters} events.
+ * This filter only hides the fact that the character data
+ * comes from a CDATA section.
+ *
+ * @author Christoph Böhme
+ *
+ */
+public final class CDataFilter extends LexicalHandlerXmlFilter {
+
+	public CDataFilter(final XMLReader parent) {
+		super(parent);
+	}
+
+	@Override
+	public void startCDATA() throws SAXException {
+		// Do not forward CDATA section events
+	}
+
+	@Override
+	public void endCDATA() throws SAXException {
+		// Do not forward CDATA section events
+	}
+
+}

src/main/java/org/culturegraph/mf/util/xml/CDataFilter.java

@@ -0,0 +1,38 @@
+/*
+ *  Copyright 2014 Christoph Böhme
+ *
+ *  Licensed under the Apache License, Version 2.0 the "License";
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+package org.culturegraph.mf.util.xml;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.XMLReader;
+
+/**
+ * Filters out {@code comment} SAX events.
+ *
+ * @author Christoph Böhme
+ *
+ */
+public final class CommentsFilter extends LexicalHandlerXmlFilter {
+
+	public CommentsFilter(final XMLReader parent) {
+		super(parent);
+	}
+
+	@Override
+	public void comment(final char[] ch, final int start, final int length) throws SAXException {
+		// Do not forward comment events
+	}
+
+}